[BioC] How to interpret the vst transformation of illumina expression data?

[Wolfgang Huber]

Dear Eva

the short answer is that you can report VST transformed data just like 
log-transformed data, and compute (estimates of) relative fold change as 
you suggest.

The slightly longer answer is that

    asinh(x) = log(x + sqrt(x^2 + 1))

and this extra term "sqrt(x^2 + 1)" only really plays a role when x is 
small (for large x, asinh(x)~log(2x)=log(x)+const.) Its role is similar 
to what is called "background correction" in approaches that are 
log-transformation based, and it makes sure that (log-)ratios between 
small intensities are regularized towards 1 (0), in order to control (or 
stabilize) the variance.

For example, the "normexp background correction" is a complicated 
non-linear transformation of the data intended to be applied before the 
log-transformation.

  Best wishes
	Wolfgang

----------------------------------------------------
Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber



Mgr. Eva Budinská wrote:
> Dear all, 
> 
>  
> 
> I am analyzing illumina data and I treat a "little" problem. If I use vst
> transformation as proposed by Simon Lin and Pan Du for normalization, I have
> a problem with interpretation of these values. 
> 
> I have 5 clinical groups, from which one is represents controls. If I apply
> log2 transformation, I can simply subtract let's say median of control group
> from all values and thus obtain a kind of ratio representing the relative
> fold change in expression. If the biologists are interested in "real", not
> logged expression, I can derive it using the 2^ function to the logarithm of
> value of relative fold change (I know this is a bit tricky, but for
> informative purposes still usable).
> 
> But when using vst, where arcsinh is used, this task is not so simple,
> especially for relative fold change in comparison to control.
> 
> How do you treat this problem?
> 
>  
> 
> Thank you very much.
> 
>  
> 
> Eva
> 
>  
> 
> *********************************************
> Eva Budinská, M.Sc.
> Institute of Biostatistics and Analyses
> Faculty of Science and Faculty of Medicine
> Masaryk University
> Kamenice 126/3, 625 00, Brno, Czech Republic
> ----------------------------
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